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- PDB-5l8r: The structure of plant photosystem I super-complex at 2.6 angstro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l8r | ||||||||||||
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Title | The structure of plant photosystem I super-complex at 2.6 angstrom resolution. | ||||||||||||
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![]() | OXIDOREDUCTASE / photosynthesis / membrane complex / chlorophyll / light harvesting | ||||||||||||
Function / homology | ![]() photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein stabilization / magnesium ion binding / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution. Authors: Mazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 50.9 MB | Display | ![]() |
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Full document | ![]() | 52.4 MB | Display | |
Data in XML | ![]() | 244.2 KB | Display | |
Data in CIF | ![]() | 280.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 5 types, 5 molecules 12CDG
#1: Protein | Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 28912.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34
#3: Protein | Mass: 29634.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#5: Protein | Mass: 84265.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 82512.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Putative uncharacterized ... , 2 types, 2 molecules EL
#9: Protein | Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#16: Protein | Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK
#10: Protein | Mass: 17238.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein/peptide | Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein/peptide | Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 7988.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 2 types, 15 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#24: Sugar | ChemComp-LMT / #26: Sugar | ChemComp-DGD / |
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-Non-polymers , 13 types, 436 molecules ![](data/chem/img/LUT.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/ZEX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/ZEX.gif)
![](data/chem/img/HOH.gif)
#17: Chemical | ChemComp-LUT / ( #18: Chemical | ChemComp-BCR / #19: Chemical | ChemComp-CLA / #20: Chemical | ChemComp-CHL / #21: Chemical | ChemComp-LHG / #22: Chemical | ChemComp-LMG / #23: Chemical | #25: Chemical | #27: Chemical | ChemComp-CL0 / | #28: Chemical | #29: Chemical | #30: Chemical | ChemComp-ZEX / ( | #31: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.75 Details: 30mM Tris-Hcl pH8.75, 50mM KH2PO4, 0.03% Octyl Glucose Neopentyl Glycol, 14% PEG400, 2mM glutathione |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 248807 / % possible obs: 99.9 % / Redundancy: 84.6 % / CC1/2: 0.997 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 83.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.906 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.038 Å / Origin y: 7.6729 Å / Origin z: 64.5628 Å
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Refinement TLS group | Selection details: all |